Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru

Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

BACKGROUND

Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called "uncultivable" microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs.

RESULTS

In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance.

CONCLUSION

Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.

Contrasting Diversity and Composition of Human Colostrum Microbiota in a Maternal Cohort With Different Ethnic Origins but Shared Physical Geography (Island Scale)

Colostrum represents an important source for the transfer of important commensal bacteria from mother to newborn and has a strong impact on the newborn’s health after birth. However, the composition of the colostrum microbiome is highly heterogeneous due to geographic factors and ethnicity (maternal, cultural, and subsistence factors). By analyzing the colostrum 16S rRNA gene full-length sequencing dataset in 97 healthy mothers (60 from Han, 37 from Li) from the Hainan island of China, we showed that the ethnic differences of the colostrum microbiome in a maternal cohort with different ethnic origins shared physical geography. Results indicated that the richness of microbial community in colostrum of Han women was higher than that of Li women, but there was no significant difference in Shannon index and invsimpson index between the two groups. Visualization analysis based on the distance showed an obvious ethnicity-associated structural segregation of colostrum microbiota. The relative abundance of Firmicutes was higher in the microbiota of the Han group than in Li’s, while Proteobacteria was on the contrary. At the genus level, the most dominant members of the Han and Li ethnic groups were Acinetobacter and Cupriavidus, two common environmental bacteria, respectively, although skin-derived Staphylococcus and Streptococcus were still subdominant taxa. Cupriavidus lacunae was the most dominant species in the Li group, accounting for 26.10% of the total bacterial community, but only 3.43% for the Han group with the most dominant Staphylococcus petrasii (25.54%), indicating that human colostrum microbiome was more susceptible to local living environmental factors. Hence, the ethnic origin of individuals may be an important factor to consider in human milk microbiome research and its potential clinical significance during the perinatal period in ethnic-diverse societies, even within a small geographic scale.

Genome-based classification of Calidifontibacillus erzurumensis gen. nov., sp. nov., isolated from a hot spring in Turkey, with reclassification of Bacillus azotoformans as Calidifontibacillus azotoformans comb. nov. and Bacillus oryziterrae as Calidifontibacillus oryziterrae comb. nov

A novel Gram-stain-positive, rod-shaped, endospore-forming, motile, aerobic bacterium, designated as P2^T, was isolated from a hot spring water sample collected from Ilica-Erzurum, Turkey. Phylogenetic analyses based on 16S rRNA gene sequence comparisons affiliated strain P2^T with the genus Bacillus, and the strain showed the highest sequence identity to Bacillus azotoformans NBRC 15712^T (96.7 %). However, the pairwise sequence comparisons of the 16S rRNA genes revealed that strain P2^T shared only 94.7 % sequence identity with Bacillus subtilis subsp. subtilis NCIB 3610^T, indicating that strain P2^T might not be a member of the genus Bacillus. The digital DNA-DNA hybridization and average nucleotide identity values between strain P2^T and B. azotoformans NBRC 15712^T were 19.8 and 74.2 %, respectively. The cell-wall peptidoglycan of strain P2^T contained meso-diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid, five unidentified phospholipids and two unidentified lipids while the predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C_15 : 0 and iso-C_16 : 0. The draft genome of strain P2^T was composed of 82 contigs and found to be 3.5 Mb with 36.1 mol% G+C content. The results of phylogenomic and phenotypic analyses revealed that strain P2^T represents a novel genus in the family Bacillaceae, for which the name Calidifontibacillus erzurumensis gen. nov., sp. nov. is proposed. The type strain of Calidifontibacillus erzurumensis is P2^T (=CECT 9886^T=DSM 107530^T=NCCB 100675^T). Based on the results of the present study, it is also suggested that Bacillus azotoformans and Bacillus oryziterrae should be transferred to this novel genus as Calidifontibacillus azotoformans comb. nov. and Calidifontibacillus oryziterrae comb. nov., respectively.

Discovery and Characterization of a Novel Thermostable β-Amino Acid Transaminase from a Meiothermus Strain Isolated in an Icelandic Hot Spring

A Meiothermus strain capable of using β-phenylalanine for growth is isolated by culture enrichment of samples collected in hot environments and the genome is sequenced showing the presence of 22 putative transaminase (TA) sequences. On the basis of phylogenetic and sequence analysis, a TA termed Ms-TA2 is selected for further studies. The enzyme is successfully produced in Escherichia coli Rosetta(DE3) cells, with 70 mg of pure protein obtained from 1 L culture after purification by affinity chromatography. Ms-TA2 shows high activity toward (S)-β-phenylalanine and other (S)-β-amino acids, as well as a preference for α-ketoglutarate and aromatic aldehydes as amino acceptors. Moreover, Ms-TA2 is shown to be a thermostable enzyme by maintaining about 60% of the starting activity after 3 h incubation at 50 °C and showing a melting temperature of about 73 °C. Finally, a homology-based structural model of Ms-TA2 is built and key active site interactions for substrate and cofactor binding are analyzed.

Bacillus pasinlerensis sp. nov., a thermophilic bacterium isolated from a hot spring in Turkey

A Gram-reaction-positive, endospore-forming bacterium, designated strain P1^T, was isolated from water samples collected from Pasinler Hot Spring and characterized using a polyphasic approach to clarify its taxonomic position. Strain P1^T was found to have chemotaxonomic and morphological characteristics consistent with its classification in the genus Bacillus. The strain shared the highest 16S rRNA gene sequence identity values with Bacillus thermolactis R-6488^T (97.6 %) and Bacillus kokeshiiformis MO-04^T (97.2 %) and formed a distinct clade with both type strains in the phylogenetic trees based on 16S rRNA gene sequences. Strain P1^T could grow optimally at 55 °C and in the presence of 2 % NaCl. The organism was found to contain meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The predominant menaquinone was determined to be MK-7. The major cellular fatty acids were identified as iso-C_15 : 0, iso-C_17 : 0 and anteiso-C_17 : 0. Based upon the consensus of phenotypic and phylogenetic analyses, strain P1^T represents a novel species of the genus Bacillus, for which the name Bacillus pasinlerensis sp. nov. is proposed. The type strain is P1^T (=DSM 107529^T=CECT 9885^T=NCCB 100674^T).

Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermus with validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus . The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov.

Multidisciplinary involvement and potential of thermophiles

The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.